Catalytic and conformational changes induced by limited subtilisin cleavage of bovine carboxypeptidase A

Crystal structure of bacteriophage ϕNIT1 zinc peptidase PghP that hydrolyzes γ-glutamyl linkage of bacterial poly-γ-glutamate

Poly-γ-glutamate hydrolase P (PghP) of Bacillus subtilis bacteriophage ΦNIT1 hydrolyzes the γ-glutamyl peptide linkage of extracellular poly-γ-glutamate produced by bacilli, which facilitates infection and propagation of phage progenies. Crystal structure of PghP was determined at a resolution of 1.9 Å. Structure of PghP was elucidated as a globular protein with an open α/β mixed core structure and a seven-stranded parallel/anti-parallel β-sheet. The β-sheet contained a core four-stranded parallel β-sheet. A zinc-binding motif, His-Glu-His, was identified at the C-terminal end of the β-sheet. Structure analysis demonstrated that PghP, which had not been previously classified into any peptidase/protease family due to lack of amino acid sequence similarity with known enzymes, had a catalytic center containing a zinc ion and an overall topology resembling mammalian carboxypeptidase A and related enzymes. Structural comparisons indicated important amino acid residues of PghP for catalysis and recognition of the γ-peptide bond of poly-γ-glutamate, which was confirmed by site-directed mutagenesis of PghP.

Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis

The metallocarboxypeptidases (MCPs) belonging to the clan MC were studied by the Optimal Docking Area (ODA) method to evaluate protein-protein binding sites and to provide a basis for the identification of binding partners for this class of enzymes. The ODA method identifies surface patches with optimal desolvation energy based on the selection of low-energy docking regions, generated from a set of surface points around the protein. With few exceptions, the ODA method identified surface patches with a significant low-energy docking surface for all the MCPs with known three-dimensional structure. Overall, in 14 out of 24 cases, the detected ODA patches were correctly located (i.e. more than 50% of the predicted residues were in known protein-protein binding sites), yielding a global success rate of 58%. More specifically, the success rate increased up to 80% on the ODA patches detected for the catalytic domains of the M14A subfamily, independently on the partner. Interestingly, the ODA residues on the catalytic domain were correctly located in the interface with the N-terminal pro domain in all MCPs. The spatial distribution of the ODA patches for the different members of the family is in relation to the origin and function of the particular MCP, which allowed distinguishing between them. In good agreement with the experimentally characterized protein interfaces, the total average surface area of the theoretically derived ODA patches for the catalytic domain of MCPs is around 1700 A2 and their content in hydrophobic residues is about 40%. As a particular case, the average surface area of the ODA patches in MCPs of crop insect pests is about twice that of the MCPs of vertebrates, which might be related to their particular function. We recognized two binding regions for the catalytic domain of the MCPs, one of them accounting for nearly all the known intermolecular interactions made up by the enzymes. Protein inhibitors seem to have evolved to dock on this subset of ODA patches, evoking the binding mode of the N-terminal pro domains. The second binding region detected, for which no ligands have been identified so far, seems to be related to the acquisition/maintenance of the native structure of the peptidase. Overall, the ODA method has been successful in identifying low-energy docking areas in a set of structurally and functionally related proteins, suggesting that it can be easily extended to other families in the search for protein-protein binding sites and for their functional significance.

Limited proteolysis of human kidney angiotensin-converting enzyme and generation of catalytically active N- and C-terminal domains

The somatic form of angiotensin converting enzyme is a class I ectoenzyme that is bound to the surface of endothelial calls. It consists of two homologous, catalytic domains of approximately 600 residues each; a juxtamembrane "stalk" region; a transmembrane, hydrophobic sequence; and a 30 residue, C-terminal cytosolic domain. We have used limited proteolysis to probe the structural and functional properties of the enzyme. Endoproteinase Asp-N cleaves both the Thr615-Asp616 and the Leu1219-Asp1220 peptide bonds to generate the two catalytic domains which were isolated by a combination of immunoaffinity and lisinopril Sepharose affinity chromatography. The enzymatic characteristics of the N and C fragments were examined with angiotensin I, hippuryl-His-Leu, and luteinizing hormone-releasing hormone and indicate that both fragments contain catalytically active sites that retain their individual functional integrity.

Chaperone-like effect of monoclonal antibodies on refolding of heat-denatured carboxypeptidase A

The availability of monoclonal antibodies which bind to a specific antigen at distinct and well-defined sites has led to a better understanding of the effects of highly specific enzyme-antibody interactions on enzyme behaviour. By appropriate selection it has been possible to isolate those antibodies that are non-inhibitory to biological activity of the enzyme and bind at strategic locations on the antigen molecule, resulting in a considerable stabilization effect on the enzyme conformation. Moreover, such monoclonal antibodies proved to have a chaperone activity leading to a considerable refolding effect on the enzyme which was already partially heat denatured. Renaturation of carboxypeptidase A after heat denaturation in the presence of selected monoclonal antibodies, was followed by recovery of its enzymatic activity. The refolding effect of anti-CPA monoclonal antibodies on heat-denatured enzyme depends on the degree of denaturation of the enzyme and on the location of the antigenic site of each antibody. The additivity effect of the pairs of monoclonal antibodies on the refolding process of CPA proved to be dependent on the localization of the antigenic sites of the monoclonal antibodies studied.

Mutations in a nonconserved sequence of the Tetrahymena ribozyme increase activity and specificity

The RNA substrate-binding site of the Tetrahymena ribozyme is connected to the catalytic core by the joining region J1/2. Although J1/2 is not conserved among group I introns, small insertions or deletions in this sequence have dramatic effects, enhancing the turnover number and sequence specificity of ribozyme-catalyzed RNA cleavage. Measurements of rate constants for individual steps in the reaction have revealed the basis of these improvements. Ironically, the higher turnover and specificity both result from decreased affinity for RNA, rather than better cleavage. These results provide evidence that the nonconserved J1/2 sequence positions the RNA substrate to optimize tertiary interactions and ensure cleavage at the position corresponding to the 5' splice site. The wild-type RNA is well adapted to its biological function, and its limitations in multiple turnover can be corrected by mutation.